RetrogeneDB ID: retro_ptro_2004

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:90789764..90790256(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CD53
• Ensembl ID: ENSPTRG00000001085
• Aliases: None
• Description: CD53 molecule [Source:HGNC Symbol;Acc:1686]

Sequence

>retro_ptro_2004
GGGATGTATCCGCTGATCCACAACAGCTTGGGAGTGCTCTTCCATAAGCTCCCCTCCCTCATGCCGGGCAATGTGCTTGT
CATCGTGGTCTCCATTATCACGATGGTTGCCTTCCTGCGCTGCATAGGTTCTGTCAAGAAAAACAGGTGCCTGCTTATGT
CCTTGTTCATTCTGCTGCCGGTTATCCTCCTTGCTGAGGTGATCTTGGCCATCCTGCACTTAGTTTACAAACGGAAGCTG
AATGTATAGGTAGCTGAGGGCCTGACAGACAGCATCTACCATTACCACTGGGACAACAGCACCAAGGTGATGTGGGACTC
CATCCAGTCATTTCTGCACTGTTGTGGCGTAAATGGCATGAGTGATTGGTCCAGCGGGCAACAAGCATCCTGCCCCTCAG
ATCCAAAAGTGAAAGGTTGCTATGCAAAAGCGAGACTGTAGTTTCACGCCAATTTCCTGTATATCAGAATCATCACCATC
TGTGTATATGTG

Alignment

ORF - retro_ptro_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 74.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIYLLIHNNFGVLFHNLPSLTLGNVFVIVGSIIMVVAFLGCMGSIKENKCLLMSFFILLLIILLAEVTLA
          G.Y.LIHN..GVLFH.LPSL..GNV.VIV.SII..VAFL.C.GS.K.N.CLLMS.FILL..ILLAEV.LA
Retrocopy GMYPLIHNSLGVLFHKLPSLMPGNVLVIVVSIITMVAFLRCIGSVKKNRCLLMSLFILLPVILLAEVILA

Parental  ILLFVYEQKLNEYVAKGLTDSIHRYHSDNSTKAAWDSIQSFLQCCGINGTSDWTSGPPASCPSDRKVEGC
          IL..VY..KLN..VA.GLTDSI..YH.DNSTK..WDSIQSFL.CCG.NG.SDW.SG..ASCPSD.KV.GC
Retrocopy ILHLVYKRKLNV*VAEGLTDSIYHYHWDNSTKVMWDSIQSFLHCCGVNGMSDWSSGQQASCPSDPKVKGC

Parental  YAKARLWFHSNFLYIGIITICVCV
          YAKARL.FH.NFLYI.IITICV.V
Retrocopy YAKARL*FHANFLYIRIITICVYV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.25 RPM	7.44 RPM
SRP007412_cerebellum	0.04 RPM	6.31 RPM
SRP007412_heart	0.12 RPM	5.19 RPM
SRP007412_kidney	0.08 RPM	9.13 RPM
SRP007412_liver	0.03 RPM	15.88 RPM
SRP007412_testis	0.11 RPM	1.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2004 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2004 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2960
Gorilla gorilla	retro_ggor_2050

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010760	2 retrocopies	retro_chof_116, retro_chof_307,
Homo sapiens	ENSG00000143119	1 retrocopy	retro_hsap_2960,
Gorilla gorilla	ENSGGOG00000005468	1 retrocopy	retro_ggor_2050,
Macaca mulatta	ENSMMUG00000000811	1 retrocopy	retro_mmul_1894,
Nomascus leucogenys	ENSNLEG00000003649	1 retrocopy	retro_nleu_1643,
Otolemur garnettii	ENSOGAG00000016713	2 retrocopies	retro_ogar_2407, retro_ogar_469,
Pan troglodytes	ENSPTRG00000001085	1 retrocopy	retro_ptro_2004 ,